[2024-01-24 11:13:04,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference
[2024-01-24 11:13:05,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,686] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bcef81f-6931-4398-981e-dc979da8a40d/GCF_025567415.1_ASM2556741v1_genomic.fna.gz | prodigal -d GCF_025567415.1_ASM2556741v1_genomic.fna/cds.fna -a GCF_025567415.1_ASM2556741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:12,328] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:12,329] [INFO] Task started: HMMsearch
[2024-01-24 11:13:12,329] [INFO] Running command: hmmsearch --tblout GCF_025567415.1_ASM2556741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/reference_markers.hmm GCF_025567415.1_ASM2556741v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:12,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:12,614] [INFO] Found 6/6 markers.
[2024-01-24 11:13:12,643] [INFO] Query marker FASTA was written to GCF_025567415.1_ASM2556741v1_genomic.fna/markers.fasta
[2024-01-24 11:13:12,644] [INFO] Task started: Blastn
[2024-01-24 11:13:12,644] [INFO] Running command: blastn -query GCF_025567415.1_ASM2556741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/reference_markers.fasta -out GCF_025567415.1_ASM2556741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:13,315] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:13,319] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:13,320] [INFO] Target genome list was writen to GCF_025567415.1_ASM2556741v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:13,508] [INFO] Task started: fastANI
[2024-01-24 11:13:13,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bcef81f-6931-4398-981e-dc979da8a40d/GCF_025567415.1_ASM2556741v1_genomic.fna.gz --refList GCF_025567415.1_ASM2556741v1_genomic.fna/target_genomes.txt --output GCF_025567415.1_ASM2556741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:22,564] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:22,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:22,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:22,579] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:22,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:22,580] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	81.8503	73	879	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.5005	195	879	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	80.1077	152	879	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	79.9639	129	879	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	79.2538	187	879	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	79.246	107	879	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	79.2278	192	879	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.1774	161	879	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.8782	146	879	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.559	211	879	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.5175	212	879	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.208	125	879	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	77.737	89	879	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.6579	56	879	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.6579	56	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:22,581] [INFO] DFAST Taxonomy check result was written to GCF_025567415.1_ASM2556741v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:22,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:22,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:22,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/checkm_data
[2024-01-24 11:13:22,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:22,617] [INFO] Task started: CheckM
[2024-01-24 11:13:22,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567415.1_ASM2556741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567415.1_ASM2556741v1_genomic.fna/checkm_input GCF_025567415.1_ASM2556741v1_genomic.fna/checkm_result
[2024-01-24 11:13:49,224] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:49,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,255] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:49,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:49,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567415.1_ASM2556741v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:49,257] [INFO] Task started: Blastn
[2024-01-24 11:13:49,257] [INFO] Running command: blastn -query GCF_025567415.1_ASM2556741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2dce49f-2cc4-4f54-a6cf-158eb69a7b2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567415.1_ASM2556741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,372] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,376] [INFO] Selected 24 target genomes.
[2024-01-24 11:13:50,377] [INFO] Target genome list was writen to GCF_025567415.1_ASM2556741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,411] [INFO] Task started: fastANI
[2024-01-24 11:13:50,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bcef81f-6931-4398-981e-dc979da8a40d/GCF_025567415.1_ASM2556741v1_genomic.fna.gz --refList GCF_025567415.1_ASM2556741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567415.1_ASM2556741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:04,253] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:04,274] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:04,275] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	97.1746	723	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	conclusive
GCA_902362865.1	s__Lachnoclostridium_B sp900066765	82.1667	198	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	99.93	99.86	0.98	0.97	3	-
GCA_000155875.1	s__Bariatricus comes	81.1787	186	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_013300725.1	s__Bariatricus comes_A	81.1741	208	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCF_001404875.1	s__Dorea_A longicatena_B	80.5888	235	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_003471165.1	s__Blautia_A sp003471165	80.4663	121	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_012524165.2	s__Muricomes sp012524165	79.9639	129	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554415.1	s__Bariatricus sp900554415	79.368	75	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCF_000169235.1	s__Dorea formicigenerans	79.2268	188	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_003435815.1	s__CAG-317 sp000433215	79.0031	202	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_018228665.1	s__UBA9414 sp003458885	78.9191	111	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCF_000154065.1	s__Dorea_A longicatena	78.5368	211	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCA_002320245.1	s__Schaedlerella sp002320245	78.4887	99	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433535.1	s__CAG-317 sp000433535	78.0977	125	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_900550865.1	s__Dorea_A sp900550865	77.9642	186	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574185.1	s__Lachnoclostridium_B sp910574185	77.9156	193	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589275.1	s__Lachnoclostridium_B sp910589275	77.7736	175	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900086725.1	s__Bariatricus massiliensis	77.7282	88	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000403455.2	s__Sporofaciens sp000403455	77.56	123	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910575605.1	s__UBA7109 sp910575605	77.5214	97	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.27	99.27	0.93	0.93	2	-
GCF_004345005.1	s__Extibacter muris	77.4749	92	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	95.70	95.67	0.77	0.77	4	-
GCA_017465565.1	s__Faecalimonas sp017465565	76.9514	73	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553885.1	s__Mediterraneibacter sp900553885	76.7459	67	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:04,276] [INFO] GTDB search result was written to GCF_025567415.1_ASM2556741v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:04,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:04,281] [INFO] DFAST_QC result json was written to GCF_025567415.1_ASM2556741v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:04,281] [INFO] DFAST_QC completed!
[2024-01-24 11:14:04,281] [INFO] Total running time: 0h0m60s